Complex relationships exist between tropical reef ecology, carbonate (CaCO 3 ) production and carbonate sinks. This paper investigates census-based techniques for determining the distribution and carbonate production of reef organisms on an emergent platform in central Torres Strait, Australia, and compares the contemporary budget with geological findings to infer shifts in reef productivity over the late Holocene. Results indicate that contemporary carbonate production varies by several orders of magnitude between and within the different reef-flat sub-environments depending on cover type and extent. Average estimated reef flat production was 1.66 ±1.78 kg m -2 yr -1 (mean ± SD) although only 23% of the area was covered by carbonate producers. Collectively, these organisms produce 17,399 ±18,618 t CaCO 3 yr -1 , with production dominated by coral (73%) and subordinate contributions by encrusting coralline algae (18%) articulated coralline algae, molluscs, foraminifera and Halimeda (<4%). Comparisons between these organisms production across the different reef flat zones, surface sediment composition and accumulation rates calculated from cores indicate that it is necessary to understand the spatial distribution, density and production of each major organism when considering the types and amounts of carbonate available for storage in the various reef carbonate sinks. These findings raise questions as to the reliability of using modal production rates in global models independent of ecosystem investigation, in particular, indicating that current models may overestimate reef productivity in emergent settings.